Analysis of a Chinese pedigree with hereditary spherocytosis caused by intron variation of SPTB gene
10.3760/cma.j.cn112140-20240930-00692
- VernacularTitle:SPTB基因内含子变异致遗传性球形红细胞增多症1家系分析
- Author:
Min HE
1
;
Rongfei LIU
1
;
Xiaoqiong WANG
1
;
Man XU
1
;
Zhigang LIU
1
Author Information
1. 西安交通大学第一附属医院儿科，西安 710061
- Publication Type:Journal Article
- Keywords:
Child;
Hereditary spherocytosis;
SPTB gene
- From:
Chinese Journal of Pediatrics
2025;63(4):411-417
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze a novel intronic variant in the SPTB gene and explore its effect on SPTB mRNA splicing.Methods:Clinical data of a child diagnosed with hereditary spherocytosis (HS) and admitted to the First Affiliated Hospital of Xi′an Jiaotong University in February 2022 were analyzed retrospectively. Whole genome sequencing was used to identify disease-causing variantions and the results were validated with Sanger sequencing, mRNA sequencing was used to determine the SPTB gene′s mRNA expression level, and bioinformatics tools were used for splicing site prediction and analysis.Results:The proband is a 2-month-old Han male child, clinically presenting with anemia and jaundice. In the past, jaundice appeared early and was severe during the neonatal period, with significantly elevated indirect bilirubin (203.5 μmol/L), accompanied by moderate anemia. This family consisted of four generations, eight of whom suffered from splenomegaly, jaundice, and anemia. In their peripheral blood, the percentage of microglobular erythrocytes was between 5% and 10%. Under scanning electron microscopy analysis of the proband's father's peripheral red blood cells, about 6% exhibited a mouth-shaped morphology, about 4% were spherical, and about 3% were oval. Following the splenectomy, the father′s anemia and jaundice recovered to normal level. Whole genome sequencing analysis of the proband identified a heterozygous variant in the SPTB gene (NM_ 001355436.2 (SPTB):c.6022+4_6022+18delinsTGGCTCCTCCGTGAAGGGACAGTCCTGC), which was verified to be co-segregating with the disease in this family line by Sanger sequencing. The results of the SPTB gene mRNA expression level detection showed that the expression levels of the SPTB variant gene were statistically increased in the proband and affected family members (father, grandmother, cousin, second cousin, great-grandmother, great-aunt) (all P<0.05). The SPTB gene′s intron can undergo selective splicing, as demonstrated by analysis using the bioinformatics program ESE Finder. Additionally, predictions from the SpliceAI and SpliceTool software indicated that activation of a new covert splicing donor can result in a code-shift variantion that introduces an early termination codon and nonsense-mediated degradation of the mRNA, which prevents the synthesis of proteins. Conclusion:A new variantion site c.6022+4_6022+18delinsTGGCTCCTCCGTGAAGGGACAGTCCTGC was found in SPTB gene. This variantion was the pathogenic factor of HS. By affecting the splicing process, this variantion triggers the nonsense mediated mRNA degradation pathway, resulting in inactivation of gene function.
